Oliver Beckstein

Yes, I downloaded the file directly from the PDB: sorry I didn’t try any others. > Am 7/8/21 um 01:26 schrieb Guillaume Fraux ***@***.***>: > > This is a bit...

@flautodipan does your mmCIF file contain a box? If I do the following with [1ake.cif](https://files.rcsb.org/download/1AKE.cif) ```python import MDAnalysis as mda from simtk.openmm.app import pdbxfile structure = pdbxfile.PDBxFile("1ake.cif") u = mda.Universe(structure)...

We have to improve our documentation to make clearer that users almost never need to do anything directly with the Readers and Converters. @lilyminium @IAlibay @fiona-naughton this might be something...

The mmCIF/PDBx format would also be needed for alphafold #3377 .

I am calling this behavior a bug because users can reasonably expect that when they set a value then it is honored. Please say something if you disagree of the...

[Your blog post](https://bfedder.github.io/jekyll/update/2022/08/14/aux-api-overhaul.html) was very useful in explaining the high level ideas. I wanted to know what happens when `auxdata=None` is provided? Does it ever make sense to do this,...

@BFedder there are a bunch of PEP8 issues https://github.com/MDAnalysis/mdanalysis/pull/3749#issuecomment-1179526826 — if you could address them then that will avoid that future developers (including future you) have to deal with them.

I think we would then - replace the `lib.util.which` function with `shutil.which` and add a deprecation note (to be removed in 3.0) - replace all use of `lib.util.which` with `shutil.which`...

You need to keep lib.util.which() but decorate it with our `deprecated` decorator (see other examples in the code). You’d replace the body of the lib.util.which() function with a call to...

Do you think that your proposed solution should be the default behavior (ie, would this be a bug fix) or should it be triggered with a kwarg?